Aux/IAA Family from Maize
Required domains for Aux/IAA family:PF02309
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Aux/IAA genes are genes that code for small nuclear proteins, 18 to 35-kD. These proteins function as transcriptional repressors by dimerizing with Auxin response factors (ARFs) that reside on auxin responsive promoter elements (AuxREs) (Luo et al., 2018). For example, ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17 (Yang et al., 2022).
Most Aux/IAA proteins have four conserved domains, I-IV.
Domain I is an active repression domain with a conserved LxLxL motif that is important for conferring repression.
Domain II interacts with an F-box protein TIR1, a component of the SCFTIR1 ubiquitin ligase complex. Auxin increases this interaction in a dose-dependent manner, promoting the rapid degradation of Aux/IAA proteins through the ubiquitin-proteasome pathway. Mutations in this domain result in increased stability of the Aux/IAA protein and increased repression of the AuxRE.
Domains III and IV have a similar amino acid sequence to motifs III and IV found in the C-terminal domains of ARF proteins, and these motifs mediate dimerization between Aux/IAA and ARF proteins (Tiwari et al., 2004).
A total of 36 ARF genes have been identified in the B73 maize genome through an iterative strategy. These genes are distributed in all maize chromosomes except chromosome 7. Maize ARF gene family expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic (Wang et al., 2010, Xing et al., 2011, Wang et al., 2012, Ludwig et al., 2013).
All but one (ZmIAA23) tested maize Aux/IAA genes were auxin inducible, displaying two types of auxin induction within three hours of treatment. Moreover, 51 of 55 (93%) differential Aux/IAA expression patterns between different root-types followed the expression tendency: crown roots > seminal roots > primary roots > lateral roots. This pattern might imply root-type-specific regulation of Aux/IAA transcript abundance. In summary, the detailed analysis of the maize Aux/IAA gene family provides novel insights in the evolution and developmental regulation and thus the function of these genes in different root-types and tissues (Ludwig et al., 2013). Variation in the the ZmIAA22 co-regulator encoded by GRMZM2G141205 (ZmIAA29) has been associated with crown root number in maize (Wang et al., 2021).
The maize Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEM 1) is a key regulator of lateral and seminal root formation. An ancient maize genome duplication resulted in the emergence of its homeolog rum1-like1 (rul1), which displays 92% amino acid sequence identity with RUM1. Both, RUL1 and RUM1 exhibit the canonical four domain structure of Aux/IAA proteins. Moreover, both are localized to the nucleus, are unstable and have similar short half-lives of ~23min. Proteins encoded by both genes interact in vivo with auxin response factors (ARFs) such as ZmARF25 and ZmARF34 in protoplasts. While RUM1 and RUL1 display conserved biochemical properties, yeast-two-hybrid in combination with BiFC experiments identified a RUM1-associated protein 1 (RAP1) that specifically interacts with RUM1 but not with RUL1. This suggests that RUM1 and RUL1 are at least in part interwoven into different molecular networks (Zhang et al., 2015).
A useful experimental system in which the nuclear Auxin Response Circuit is recapitulated in yeast (Saccharomyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, has been developed (Ramos Báez et al., 2020)
Last updated June 2023 by John Gray
Tiwari SB, Hagen G, Guilfoyle TJ. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell. 2004 Feb;16(2):533-43. doi: 10.1105/tpc.017384. Epub 2004 Jan 23. PMID: 14742873; PMCID: PMC341922.
Xing H, Pudake RN, Guo G, Xing G, Hu Z, Zhang Y, Sun Q, Ni Z. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize. BMC Genomics. 2011 Apr 7;12:178. doi: 10.1186/1471-2164-12-178. PMID: 21473768; PMCID: PMC3082248.
Wang Y, Deng D, Bian Y, Lv Y, Xie Q. Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea mays. L.). Mol Biol Rep. 2010 Dec;37(8):3991-4001. doi: 10.1007/s11033-010-0058-6. Epub 2010 Mar 16. PMID: 20232157.
Wang Y, Deng D, Shi Y, Miao N, Bian Y, Yin Z. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes. Mol Biol Rep. 2012 Mar;39(3):2401-15. doi: 10.1007/s11033-011-0991-z. Epub 2011 Jun 11. PMID: 21667107.
Ludwig Y, Zhang Y, Hochholdinger F. The maize (Zea mays L.) AUXIN/INDOLE-3-ACETIC ACID gene family: phylogeny, synteny, and unique root-type and tissue-specific expression patterns during development. PLoS One. 2013 Nov 1;8(11):e78859. doi: 10.1371/journal.pone.0078859. PMID: 24223858; PMCID: PMC3815225.
Li J, Wu F, He Y, He B, Gong Y, Yahaya BS, Xie Y, Xie W, Xu J, Wang Q, Feng X, Liu Y, Lu Y. Maize Transcription Factor ZmARF4 Confers Phosphorus Tolerance by Promoting Root Morphological Development. Int J Mol Sci. 2022 Feb 21;23(4):2361. doi: 10.3390/ijms23042361. PMID: 35216479; PMCID: PMC8880536.
Luo J, Zhou JJ, Zhang JZ. Aux/IAA Gene Family in Plants: Molecular Structure, Regulation, and Function. Int J Mol Sci. 2018 Jan 16;19(1):259. doi: 10.3390/ijms19010259. PMID: 29337875; PMCID: PMC5796205.
Yang F, Shi Y, Zhao M, Cheng B, Li X. ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17. PeerJ. 2022 Jul 14;10:e13710. doi: 10.7717/peerj.13710. PMID: 35855434; PMCID: PMC9288822.
Wang H, Tang X, Yang X, Fan Y, Xu Y, Li P, Xu C, Yang Z. Exploiting natural variation in crown root traits via genome-wide association studies in maize. BMC Plant Biol. 2021 Jul 23;21(1):346. doi: 10.1186/s12870-021-03127-x. PMID: 34301195; PMCID: PMC8299645.
Zhang Y, Marcon C, Tai H, von Behrens I, Ludwig Y, Hey S, Berendzen KW, Hochholdinger F. Conserved and unique features of the homeologous maize Aux/IAA proteins ROOTLESS WITH UNDETECTABLE MERISTEM 1 and RUM1-like 1. J Exp Bot. 2016 Feb;67(4):1137-47. doi: 10.1093/jxb/erv519. Epub 2015 Dec 15. PMID: 26672614; PMCID: PMC4753850.
Ramos Báez R, Buckley Y, Yu H, Chen Z, Gallavotti A, Nemhauser JL, Moss BL. A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit. Plant Physiol. 2020 Apr;182(4):1713-1722. doi: 10.1104/pp.19.01475. Epub 2020 Mar 2. PMID: 32123041; PMCID: PMC7140906.